Virulence regulation of phytopathogenic fungi by ph

15 p.- 6 fig.Significance: Postharvest pathogens can start its attack process immediately after spores land on wounded tissue, whereas other pathogens can forcibly breach the unripe fruit cuticle and then remain quiescent for months until fruit ripens and then cause major losses. Recent Advances: Postharvest fungal pathogens activate their development by secreting organic acids or ammonia that acidify or alkalinize the host ambient surroundings. Critical Issues: These fungal pH modulations of host environment regulate an arsenal of enzymes to increase fungal pathogenicity. This arsenal includes genes and processes that compromise host defenses, contribute to intracellular signaling, produce cell wall-degrading enzymes, regulate specific transporters, induce redox protectant systems, and generate factors needed by the pathogen to effectively cope with the hostile environment found within the host. Further, evidence is accumulating that the secreted molecules (organic acids and ammonia) are multifunctional and together with effect of the ambient pH, they activate virulence factors and simultaneously hijack the plant defense response and induce program cell death to further enhance their necrotrophic attack. Future Directions: Global studies of the effect of secreted molecules on fruit pathogen interaction, will determine the importance of these molecules on quiescence release and the initiation of fungal colonization leading to fruit and vegetable losses. © 2013, Mary Ann Liebert, Inc.We acknowledge the support of the US-Israel Binational Agricultural Research and Development Fund (BARD) during several stages of our work.Peer reviewe

Genome-Wide Survey of Cold Stress Regulated Alternative Splicing in <i>Arabidopsis thaliana</i> with Tiling Microarray

<div><p>Alternative splicing plays a major role in expanding the potential informational content of eukaryotic genomes. It is an important post-transcriptional regulatory mechanism that can increase protein diversity and affect mRNA stability. Alternative splicing is often regulated in a tissue-specific and stress-responsive manner. Cold stress, which adversely affects plant growth and development, regulates the transcription and splicing of plant splicing factors. This can affect the pre-mRNA processing of many genes. To identify cold regulated alternative splicing we applied Affymetrix <i>Arabidopsis</i> tiling arrays to survey the transcriptome under cold treatment conditions. A novel algorithm was used for detection of statistically relevant changes in intron expression within a transcript between control and cold growth conditions. A reverse transcription polymerase chain reaction (RT-PCR) analysis of a number of randomly selected genes confirmed the changes in splicing patterns under cold stress predicted by tiling array. Our analysis revealed new types of cold responsive genes. While their expression level remains relatively unchanged under cold stress their splicing pattern shows detectable changes in the relative abundance of isoforms. The majority of cold regulated alternative splicing introduced a premature termination codon (PTC) into the transcripts creating potential targets for degradation by the nonsense mediated mRNA decay (NMD) process. A number of these genes were analyzed in NMD-defective mutants by RT-PCR and shown to evade NMD. This may result in new and truncated proteins with altered functions or dominant negative effects. The results indicate that cold affects both quantitative and qualitative aspects of gene expression.</p></div

Clustergram representing correlation between transcriptomes from cold treatment conditions and stress treated plants.

<p>The transcriptomes of the WGA (2h, 10h, and 24h) experiments are clustered according to their similarity to each stress index, which are shown on the horizontal axis. The indexes for drought, osmotic, salt, cold and heat stress are from Kilian <i>et al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066511#pone.0066511-Kilian1" target="_blank">[4]</a>. The transcriptomes screened by vector-based analysis are shown on the vertical axis. Correlation values are color-coded from blue (negative correlation) to red (positive correlation). Neutral correlation values are white. The data for 2h and 10h were obtained from Matsui <i>et al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066511#pone.0066511-Matsui1" target="_blank">[11]</a></p

A sample list of detected transcripts with putative stress-regulated alternative splicing.

<p>The listed genes were used for validation of predicted cold-regulated alternative splicing events by RT-PCR. All genes, except AT1G47530, were not defined as cold responsive based on showing less than 2 and more than -2 fold change (FDR <0.05).</p>a<p>Example of cold responsive gene.</p>b<p>Alternative splicing types are intron retention (r) or unknown (u, possible exon skipping, alternative 5'/3' or intron retention).</p>c<p>The alternatively spliced intron is not completely excised in either cold treatment or control (ctrl).</p>d<p>Predictions that were confirmed by RT-PCR.</p

Flowchart of the algorithm used for detecting stress-regulated genes and alternative splicing (see text).

<p>Flowchart of the algorithm used for detecting stress-regulated genes and alternative splicing (see text).</p

Defining splicing type according to probes expression level.

<p>The common forms of alternative splicing represented here are; exon skipping, intron retention, alternative 3' acceptor site and alternative 5' donor site. Boxes joined by lines represent the exons and introns, respectively, of immature transcripts; diagonal lines indicate splicing patterns. Highly expressed probes are depicted as short thick bars while probes with low expression are depicted as short thin bars below the transcript. The splicing variant (right side) is defined as intron retention when all probes in an intron are significantly highly expressed, i.e., have near exon level expression. All other cases of altered intron probes expression are defined as unknown, as the splicing variant can include exon skipping, intron retention or alternative 5' or 3'.</p

Example of EST or cDNA evidence from TAIR genome browser supporting predicted alternative splicing type.

<p>A red rectangle marks the EST or cDNA sequence supporting the predicted alternative splicing of the sample genes <i>AT1G47530</i>, <i>AT3G06620</i> and <i>AT3G47630</i> (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0066511#pone-0066511-t001" target="_blank">Table 1</a>).</p